1. A little bit of chemistry...
Unit 1: Biochemistry
A little bit of chemistry...

2. Atoms and Electrons
Atoms are made up of protons, neutrons and electrons.
Protons and neutrons are found in the nucleus.
Electrons orbit the nucleus at different energy levels.
2 electrons fit in the first, up to 8 in the 2nd and up to 18 in the 3rd (or 8)...
The outermost electrons are known as valence electrons.

3. Bonding
If the valence electron shell is full, the electrons are paired up and stable and the atom does not react with others to form bonds.
If the outer shell is not full, and some valence electrons are unpaired, they will look for electrons elsewhere, to become more stable.
Lewis Dot diagrams show only the valence electrons and are helpful for predicting chemical reactions that will occur between atoms.

4. Types of Bonds
Ionic bond: a force of attraction between a cation and an anion.
Cation: when an atom loses an electron and becomes positively charged (ca'+'ion)‏
Anion: when an atom gains an electron and becomes negatively charge (a'negative'ion)‏
Electrons are not lost into space, when one atom loses an electron, another atom is gaining it, the separation of charge causes the two ions formed to move together, forming an ionic bond
Ex. NaCl

5. Covalent bond: when neither atoms is willing to totally give up electrons so electron pairs are shared between two atoms, rather than lost and gained. Single, double and triple bonds can results depending on how many e' pairs are shared.
ex. H2
ex. O2
ex. N2
covalent bonds are stronger than ionic bonds.

6. Electronegativity
A measure of an atom's ability to attract a shared electron pair when it is participating in a covalent bond.
Sharing is not always equal. If one atom is stronger in electronegativity that the other atom, the 'shared' electron pair will spend more time with it, and therefore that atom will have a partial negative charge ( -). The 'weaker' atom will take on a partial positive charge ( +). This type of bond is now a polar covalent bond.
When the sharing is virtually equal the bond is known as a nonpolar covalent bond.

7. Intramolecular bonds: bonds within a molecule (ionic and covalent)‏
Intermolecular bonds: bonds between molecules, aka van der Waals forces
London dispersion forces – attraction due to temporary unequal distribution of e-'s
Dipole-dipole forces – attraction due to partial separation of charge in a molecule
Hydrogen bonds – attraction between an + H and a – N, O or F in a neighbouring polar molecule.
intra are stronger than inter
weakest to strongest

8. Water so common and yet amazing in its properties solid, liquid or gas
polar covalent
allows it to make intermolecular bonds with other molecules
most importantly HYDROGEN BONDS
versatile solvent (polar molecules are hydrophilic, nonpolar are hydrophobic)‏
clings
absorbs heat
less dense as a solid than liquid
Read about water and its properties, page Answer question handout.

9. Carbon virtually all chemicals of life are carbon based
compounds that contain Carbon (and usually also hydrogen) are called organic compounds. (Note: this excludes H2O and CO2)‏
compounds that do not contain Carbon are called inorganic.
The major classes of organic compounds are: carbs, lipids, proteins and nucleic acids.

10. Hydrocarbons
Carbon has four single valence electrons, therefore it can form up to four covalent bonds with other atoms.
Carbon atoms attach to each other to form straight and branched chains and ring structures that are the backbones of biological molecules.
The other electrons often form bonds with hydrogen, hydrocarbons are molecules containing carbon and hydrogen ONLY.
Hydrocarbons are non-polar due to the symmetry of their arrangement (see board).

11. Functional Groups
Other elements may attach to the carbon backbone to form reactive clusters of atoms called functional groups.
These groups are more reactive than the hydrocarbon chains an impart certain chemical properties to the molecule.
-OH and -COOH are polar because of the oxygen atom, making compounds that contain them (alcohols and sugars) highly soluble in water.
study the group name, chemical formula and structural formula, we will be learning about the molecules they are found in.